1YRS

Crystal structure of KSP in complex with inhibitor 1

• PDB DOI:  https://doi.org/10.2210/pdb1YRS/pdb

• Classification: CELL CYCLE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2005-02-04 Released: 2005-04-12 
• Deposition Author(s): Cox, C.D., Breslin, M.J., Mariano, B.J., Coleman, P.J., Buser, C.A., Walsh, E.S., Hamilton, K., Kohl, N.E., Torrent, M., Yan, Y., Kuo, L.C., Hartman, G.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.310 
• R-Value Work: 0.250 
• R-Value Observed: 0.250 

Literature

Kinesin spindle protein (KSP) inhibitors. Part 1: The discovery of 3,5-diaryl-4,5-dihydropyrazoles as potent and selective inhibitors of the mitotic kinesin KSP

Cox, C.D., Breslin, M.J., Mariano, B.J., Coleman, P.J., Buser, C.A., Walsh, E.S., Hamilton, K., Huber, H.E., Kohl, N.E., Torrent, M., Yan, Y., Kuo, L.C., Hartman, G.D.

(2005) Bioorg Med Chem Lett 15: 2041-2045

• PubMed: 15808464 
• DOI: https://doi.org/10.1016/j.bmcl.2005.02.055
• Primary Citation of Related Structures:  
  1YRS


• PubMed Abstract: 
  

Optimization of high-throughput screening (HTS) hits resulted in the discovery of 3,5-diaryl-4,5-dihydropyrazoles as potent and selective inhibitors of KSP. Dihydropyrazole 15 is a potent, cell-active KSP inhibitor that induces apoptosis and generates aberrant mitotic spindles in human ovarian carcinoma cells at low nanomolar concentrations. X-ray crystallographic evidence is presented which demonstrates that these inhibitors bind in an allosteric pocket of KSP distant from the nucleotide and microtubule binding sites.

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Organizational Affiliation: 

Department of Medicinal Chemistry, Merck Research Laboratories, PO Box 4, Sumneytown Pike, West Point, PA 19486, USA. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 83.64 kDa 
• Atom Count: 5,454 
• Modelled Residue Count: 660 
• Deposited Residue Count: 736 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Kinesin-like protein KIF11	A, B	368	Homo sapiens	Mutation(s): 0  Gene Names: KIF11, EG5, KNSL1, TRIP5
UniProt & NIH Common Fund Data Resources
Find proteins for P52732 (Homo sapiens) Explore P52732  Go to UniProtKB:  P52732
PHAROS:  P52732

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	D [auth A], G [auth B]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
L47	E [auth A], H [auth B]	3-[(5S)-1-ACETYL-3-(2-CHLOROPHENYL)-4,5-DIHYDRO-1H-PYRAZOL-5-YL]PHENOL C17 H15 Cl N2 O2 QBZAPFWYAPXRGQ-KRWDZBQOSA-N
MG	C [auth A], F [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
L47	Binding MOAD:  1YRS	IC50: 450 (nM) from 1 assay(s)
	PDBBind:  1YRS	IC50: 450 (nM) from 1 assay(s)
	BindingDB:  1YRS	IC50: 450 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.310 
• R-Value Work: 0.250 
• R-Value Observed: 0.250 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.3	α = 90
b = 79.8	β = 90
c = 159.6	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
CNS	refinement
HKL-2000	data reduction
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-04-12 
Deposition Author(s): Cox, C.D., Breslin, M.J., Mariano, B.J., Coleman, P.J., Buser, C.A., Walsh, E.S., Hamilton, K., Kohl, N.E., Torrent, M., Yan, Y., Kuo, L.C., Hartman, G.D.

Revision History  

• Version 1.0: 2005-04-12
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-08-23
  Changes: Data collection, Database references, Derived calculations, Refinement description